Definitely use the cruise ships transfers. Even at $100 pp it is worth the aggrevation you will find in getting there from San Diego. I live in San Diego and have my whole life and I will tell you that while I have been to Mexico too many times to count and feel that I "know" my way around well enough I would still take the Cruise Transport.
Here are a few of the reasons:
1. Immigration Issues
2. Toll Road
3. Getting Lost bc they have changed the route or the road
4. Road Bandits
5. Hassle of changing cabs at Border
6. You have to walk across the border with all your luggage
So take it from someone that has more experience in these matters - Do not try to save a few bucks, just use the cruise lines mode of transport.